Align L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 (characterized)
to candidate AO353_25960 AO353_25960 threonine dehydratase
Query= SwissProt::Q9WYJ1 (401 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25960 Length = 336 Score = 241 bits (615), Expect = 2e-68 Identities = 127/301 (42%), Positives = 194/301 (64%), Gaps = 4/301 (1%) Query: 20 RTALAYSSVLSEVTGGEIYLKMENLQKTGSFKIRGAYNKIAHLSEEERKRGVVAASAGNH 79 RT L + LSEV G +I LK E+LQ T SFKIRGAYNK+A LS E++ RGV+ ASAGNH Sbjct: 33 RTPLQVAPALSEVLGNQILLKREDLQPTFSFKIRGAYNKLAQLSAEQKARGVITASAGNH 92 Query: 80 AQGVALAAQIFGIPATIVMPRYAPLSKITKTRNLGAQVILEGNIFDEAYEAALRIQEKTG 139 AQGVALAA+ GI A+IVMP P K+ R+ GA +L G F A E AL + +TG Sbjct: 93 AQGVALAARELGIEASIVMPTSTPELKVIGVRSRGANAVLHGESFPFALEYALNLARQTG 152 Query: 140 AVFVHPFNDPHVIAGQGTIGLEIM-EDLPDVEVVVVPVGGGGLISGVSVAIKSMNPEVKV 198 FV PF+DP VIAGQGT+ +EI+ + ++ + VPVGGGGLI+G++ +K + PE+++ Sbjct: 153 RTFVSPFDDPDVIAGQGTVAMEILRQHQGALDAIFVPVGGGGLIAGIAAYVKYLRPEIRI 212 Query: 199 IGVQTENMPSMIASLRRGRAERVEGKPTLADGIAVKKPGDLTFELVKKYVDEMVAVNEEE 258 +GV++E+ + A++ G + T ADG+AV + G+ FE+ + +VDE++ V+ +E Sbjct: 213 VGVESEHSACLQAAMLAGERVVLPKVGTFADGVAVAQIGEYGFEICRHHVDEVLTVSNDE 272 Query: 259 IADAILFLLEQAKVVAEGAGAVGVAAV---LNKLDVKGKKVAIVISGGNIDVNMIDRIIN 315 + AI + + + + E +GA+ VA + + + V+G+ + + SG NI+ + + + Sbjct: 273 LCAAIKNIYDDTRSITEPSGALAVAGIKKYVAQTGVRGQTLVAIDSGANINFDSLRHVAE 332 Query: 316 K 316 + Sbjct: 333 R 333 Lambda K H 0.317 0.136 0.367 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 278 Number of extensions: 12 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 401 Length of database: 336 Length adjustment: 30 Effective length of query: 371 Effective length of database: 306 Effective search space: 113526 Effective search space used: 113526 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
Align candidate AO353_25960 AO353_25960 (threonine dehydratase)
to HMM TIGR01124 (ilvA: threonine ammonia-lyase, biosynthetic (EC 4.3.1.19))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR01124.hmm # target sequence database: /tmp/gapView.11182.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01124 [M=499] Accession: TIGR01124 Description: ilvA_2Cterm: threonine ammonia-lyase, biosynthetic Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-153 497.3 2.3 2.5e-153 497.2 2.3 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_25960 AO353_25960 threonine dehydratas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_25960 AO353_25960 threonine dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 497.2 2.3 2.5e-153 2.5e-153 2 319 .. 18 335 .. 17 336 .] 0.99 Alignments for each domain: == domain 1 score: 497.2 bits; conditional E-value: 2.5e-153 TIGR01124 2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkak 66 y+++il a vye av tpl+ a lse l+n++llkredlqp fsfk+rGaynk+aqlsaeqka+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_25960 18 YVKKILAAPVYELAVRTPLQVAPALSEVLGNQILLKREDLQPTFSFKIRGAYNKLAQLSAEQKAR 82 899************************************************************** PP TIGR01124 67 GviaasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalel 131 Gvi+asaGnhaqGval+a++lG++a ivmp++tpe+kv v+++G++ vlhGe++ a ++al+l lcl|FitnessBrowser__pseudo3_N2E3:AO353_25960 83 GVITASAGNHAQGVALAARELGIEASIVMPTSTPELKVIGVRSRGANAVLHGESFPFALEYALNL 147 ***************************************************************** PP TIGR01124 132 aqekgltfiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikv 196 a++ g tf++pfddp+viaGqGtva+e+lrq++ lda+fvpvGGGGliaG+aa+vk l+pei++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_25960 148 ARQTGRTFVSPFDDPDVIAGQGTVAMEILRQHQGALDAIFVPVGGGGLIAGIAAYVKYLRPEIRI 212 ***************************************************************** PP TIGR01124 197 igveaedsaalkqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaai 261 +gve+e sa+l++a+ aGerv l +vG fadGvav ++G++ f++c++++d++++v de+caai lcl|FitnessBrowser__pseudo3_N2E3:AO353_25960 213 VGVESEHSACLQAAMLAGERVVLPKVGTFADGVAVAQIGEYGFEICRHHVDEVLTVSNDELCAAI 277 ***************************************************************** PP TIGR01124 262 kdvfedtravlepaGalalaGlkkyvakkgiedktlvailsGanlnfdrlryvserae 319 k++++dtr+++ep+Gala+aG+kkyva+ g++++tlvai sGan+nfd+lr+v+era lcl|FitnessBrowser__pseudo3_N2E3:AO353_25960 278 KNIYDDTRSITEPSGALAVAGIKKYVAQTGVRGQTLVAIDSGANINFDSLRHVAERAA 335 ********************************************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (499 nodes) Target sequences: 1 (336 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 8.25 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory